6GNL

Zr(IV)-substituted Keggin directly binding to the side chain of Hen Egg-White Lysozyme (HEWL)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Direct observation of the ZrIVinteraction with the carboxamide bond in a noncovalent complex between Hen Egg White Lysozyme and a Zr-substituted Keggin polyoxometalate.

Vandebroek, L.Van Meervelt, L.Parac-Vogt, T.N.

(2018) Acta Crystallogr C Struct Chem 74: 1348-1354

  • DOI: https://doi.org/10.1107/S2053229618010690
  • Primary Citation of Related Structures:  
    6GNL

  • PubMed Abstract: 

    The successful cocrystallization of the noncovalent complex formed between (Et 2 NH 2 ) 8 [{α-PW 11 O 39 Zr-(μ-OH)(H 2 O)} 2 ]·7H 2 O Keggin polyoxometalate (2) and Hen Egg White Lysozyme (HEWL) protein is reported. The resulting structural model revealed interaction between monomeric [Zr(PW 11 O 39 )] 4- (1), which is a postulated catalytically active species, and the protein in two positions in the asymmetric unit. The first position (occupancy 36%) confirms the previously observed binding sites on the protein surface, whereas the second position (occupancy 14%) provides novel insights into the hydrolytic mechanisms of Zr IV -substituted polyoxometalates. The new interaction site occurs at the Asn65 residue, which is directly next to the Asp66-Gly67 peptide bond that was identified recently as a cleavage site in the polyoxometalate-catalysed hydrolysis of HEWL. Furthermore, in this newly discovered binding site, the monomeric polyoxometalate 1 is observed to bind directly to the side chain of the Asn65 residue. This binding of Zr IV as a Lewis-acid metal to the carbonyl O atom of the Asn65 side chain is very similar to the intermediate state proposed in density functional theory (DFT) studies in which Zr IV activates the peptide bond via interaction with its carbonyl O atom, and can be thus regarded as a model for interaction between Zr IV and a peptide bond.


  • Organizational Affiliation

    Department of Chemistry, KU Leuven, Celestijnenlaan 200F box 2404, Leuven 3001, Belgium.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.701α = 90
b = 77.701β = 90
c = 37.866γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2018-11-14
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description